[BioC] Any package to calculate NGS coverage and plot it?

[Xiaohui Wu]

Dear list,

I have some NGS sequences that enriched in different regions along the genome. I want to calculate the coverage of the short sequences and plot the sequences  in a specific region. To plot, I just want a function to simply plot the tags and chromosome (it is OK if also plot the gene there), but not other things like in genome browser. Is there any package can do this? 
Thank you!

Best,
Xiaohui